Yes, you shouldn’t use it in your theme. It’s used in WP core on administration side for adding touch scripts, mobile button etc. It’s very dumb, it just detects User Agent string which can anybody change. And the biggest why not to use it is that you can have a trouble if you use it with a cache plugin because it can show mobile version when desktop version should showed.. It’s safe to use it in backend because all caching plugins caching only frontend not backend.
I think that the safest method would be input all content and show/hide whatever you want via media queries.